Season Two opens with the team on the run from the FBI. But they are caught and discover that Kimberly Grant has negotiated a deal for them.

Under the leadership of Jake Shaw, the team (Steve, Julie, Brandon, Page, Tasha, and now Damien) begin working for the government under Operation: Mega Force. They continue to live in the Grant Gardens Apartment Complex and Kimberly Grant remains an ally, but becomes relatively hands off.

The main antagonists this season are Shiftess's gang, and BioGen Labs, which has branched out into cybernetics and other technologies such as temporal and dimensional travel. The team also meets many other tainted people and make new allies.